Dear AMBER team,
I prepared prmtop and inpcrd files for metalloprotein but got the subject
error in parmed checkvalidity with solvated system and not with the dry
system.
So, please let me know if I need to fix this error before proceeding with
MD.
Thank you and best regards,
> checkValidity
Determining validity of prmtop
2 total warnings
ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not
contiguous!
MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
Angstroms. Rename CYS to CYX in the PDB file and use the
'bond' command in tleap to create the disulfide bond
> netCharge
The net charge of :* is -0.0000
> chamber
Action chamber failed
InputError: chamber requires a PSF file
> energy
Computing a single-point energy for 2hi4-BHF-solv.prmtop
AmberWarning: Molecule atoms are not contiguous! I am attempting to reorder
the atoms to fix this.
Bond = 1978946.5672933 Angle = 14664.1737001
Dihedral = 6070.5463390 1-4 vdW = 56855.5566437
1-4 Elec = 18273.3433289 vdWaals = 18425992.7532661
Elec. = -185621.0533003
TOTAL = 20315181.8872707
> quit
Done!
(base) [vaibhav.hpc MD-simulations-CYP450]$ parmed -p 2hi4-BHF-dry.prmtop
-c 2hi4-BHF-dry.inpcrd
____ .---. ,-----. _____
.' `,.': :'' : :.' `.
| : : ' ' ' ' : : \
| ' ' ' ' \
| v \
| | v \
| | | v \
| P | A | R | M | \
| | | | | \
| | | | | \
| | | | | \
| ===== | | | | )
\ --- /| ===== | | | /
`---' \ --- /| ===== | ===== | /
`---' \ ---- A ----- / /
`----'.`-----' /
/ /
'-._ ED /
'. /
`----'
ParmEd: a Parameter file Editor
Loaded Amber topology file 2hi4-BHF-dry.prmtop with coordinates from
2hi4-BHF-dry.inpcrd
Reading input from STDIN...
> checkValidity
Determining validity of prmtop
1 total warnings
MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
Angstroms. Rename CYS to CYX in the PDB file and use the
'bond' command in tleap to create the disulfide bond
>
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Fri Jul 19 2024 - 06:30:02 PDT
